3PNI - JenaLib

Title :   CRYSTAL STRUCTURE OF D14C [3FE-4S] PYROCOCCUS FURIOSUS FERREDOXIN

Authors :   M. N. Loevgreen, H. E. M. Christensen, P. Harris

Date :   19 Nov 10 (Deposition) - 13 Apr 11 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A (1x),B (1x)

Keywords :   Ferredoxin, Iron-Sulfur Cluster, Pyrococcus Furiosus, Two Molecules In Asymmetric Unit, Electron Transport, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. N. Lovgreen, M. Martic, M. S. Windahl, H. E. Christensen, P. Harris
Crystal Structures Of The All Cysteinyl Coordinated D14C Variant Of Pyrococcus Furiosus Ferredoxin: [4Fe-4S] <-> [3Fe-4S] Cluster Conversion
J. Biol. Inorg. Chem. V. 16 763 2011
PubMed-ID: 21484348 | Reference-DOI: 10.1007/S00775-011-0778-7

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:11 , ILE A:12 , CYS A:14 , ALA A:15 , ILE A:16 , CYS A:17 , ALA A:33 , CYS A:56	BINDING SITE FOR RESIDUE F3S A 70
2	AC2	SOFTWARE	GLU A:41 , ILE B:12	BINDING SITE FOR RESIDUE CO A 75
3	AC3	SOFTWARE	SER B:59	BINDING SITE FOR RESIDUE CO B 76
4	AC4	SOFTWARE	CYS B:11 , ILE B:12 , GLY B:13 , CYS B:14 , ALA B:15 , ILE B:16 , CYS B:17 , ALA B:33 , CYS B:56	BINDING SITE FOR RESIDUE F3S B 70
5	AC5	SOFTWARE	MET B:27	BINDING SITE FOR RESIDUE CO B 75
6	AC6	SOFTWARE	SER A:59 , GLU B:38	BINDING SITE FOR RESIDUE CO B 67

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_PYRFU	3-31 36-67	4	A:2-30 B:2-30 A:35-66 B:35-66

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_PYRFU	3-31 36-67	2	A:2-30 - A:35-66 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_PYRFU	3-31 36-67	2	- B:2-30 - B:35-66

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	FER_PYRFU	3-31 36-67	4	A:2-30 B:2-30 A:35-66 B:35-66

Exons (0, 0)

Sequences/Alignments

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:66
 aligned with FER_PYRFU | P29603 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    11        21        31        41        51        61      
             FER_PYRFU    2 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 67
               SCOP domains d3pnia_ A: Fe3S4-ferredoxin PF1909                                 SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..................eee.....eee......hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: A:2-30     ----4FE4S_FER_2  PDB: A:35-66        PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3pni A  1 AWKVSVDQDTCIGCAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 66
                                    10        20        30        40        50        60

Chain B from PDB  Type:PROTEIN  Length:66
 aligned with FER_PYRFU | P29603 from UniProtKB/Swiss-Prot  Length:67

    Alignment length:66
                                    11        21        31        41        51        61      
             FER_PYRFU    2 AWKVSVDQDTCIGDAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 67
               SCOP domains d3pnib_ B: Fe3S4-ferredoxin PF1909                                 SCOP domains
               CATH domains ------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----Fer4_13-3pniB01 B:6-63                                    --- Pfam domains (1)
           Pfam domains (2) -----Fer4_13-3pniB02 B:6-63                                    --- Pfam domains (2)
         Sec.struct. author .eeeee..................eee.....eee......hhhhhhhhhhhhhhh....eeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -4FE4S_FER_2  PDB: B:2-30     ----4FE4S_FER_2  PDB: B:35-66        PROSITE
                 Transcript ------------------------------------------------------------------ Transcript
                  3pni B  1 AWKVSVDQDTCIGCAICASLCPDVFEMNDEGKAQPKVEVIEDEELYNCAKEAMEACPVSAITIEEA 66
                                    10        20        30        40        50        60

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (7, 7)

Asymmetric Unit(hide GO term definitions)

Chain A,B (FER_PYRFU | P29603)

molecular function
	GO:0051538	3 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 3 iron, 4 sulfur (3Fe-4S) cluster; this cluster consists of three iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. It is essentially a 4Fe-4S cluster with one iron missing.
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0005506	iron ion binding	Interacting selectively and non-covalently with iron (Fe) ions.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

Visualization

Interactive Views

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		F3S	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pni)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	3pni
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	FER_PYRFU \| P29603
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	FER_PYRFU \| P29603
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description